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Re: How do OBO ontologies work on the LOD?

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Wed, 22 Feb 2012 00:27:43 -0500
Message-ID: <CAFKQJ8m6VjXWYAY3Q6qmO8dVeUz85txce+ON=Jk4YONUGA_rCQ@mail.gmail.com>
To: Peter DeVries <pete.devries@gmail.com>
Cc: Juan Sequeda <juanfederico@gmail.com>, public-lod@w3.org, Chris Mungall <cjmungall@lbl.gov>
On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries <pete.devries@gmail.com>wrote:

> Hi Juan,
>
> Thanks for this. I read the paper. They have an "OWL" version of this OBO
> vocabulary but it seems to not be a fully mapped OWL version as described
> in your paper.
>

Which one?


>
> In this particular use case I was thinking of applying the terms and
> properties described by the ontology to my species concepts.
>

This is a nice example and should be supported. An immediate suggestion is
to send mail to  obo-discuss@lists.sourceforge.net as that is where you
will find both the developers of the OBO LOD support as well as the
biologist community.


>
> For instance:
>
> species X has this metabolic pathway.  (which would be useful for finding
> species with potential drug interactions or other chemical reactions)
>

We're in the process of revising BFO and the relations ontology. A draft
version is at http://purl.obolibrary.org/obo/bfo.owl

In terms of that, your statement might be represented as

<species> subclassOf 'has site of' some <metabolic process>
if you want to represent that all members of the species have the process

or

<anonymous instance of species> 'has site of'  <anonymous instance of
process>

e.g.

@prefix obo: <http://purl.obolibrary.org/obo/>
@prefix hasSiteOf: <http://purl.obolibrary.org/obo/BFO_0000067>

_:a rdf:type <species>
_:b rdf:type <metabolic process>
_:a hasSiteOf: _:b

If you want to represent that the process happens in some individuals of
this species.

In the above I write <species> where you would write the uri of your
species class (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9903) , and
<metabolic process> where you would write the uri of your process class
(e.g. http://purl.obolibrary.org/obo/GO_0030245).



> I don't think this use case requires the full OBO  relationships, just a
> mapping ontology that connects terms and characters to those in the OBO
> ontology.
>

Not sure what you mean by this.


>
> Doing it this way you might get a species "tagged" with something that is
> not appropriate but that could be detected by some service that analyzes
> the statements made
> in the species concept markup
>

Example?

> .
> My guess is that some of the OBO ontologies (if fully entailed) will not
> play well on the LOD cloud, but they would play a useful role when mapped
> as I described.
>

Examples would be helpful. But note that it is our intention that we *do*
play well on the LOD cloud. However also note, we work in OWL and much of
what we say is about types/classes, and many(most?) linked data browsers
don't understand or present OWL in a meaninful way. One of the reasons we
have developed ontobee is that it is designed to do justice to linked
ontology terms that are defined in terms of OWL. So class expressions are
not left as messes of bnodes, but instead parsed and displayed as OWL. I'd
like to see more linked data browsers do the same.


> Does my interpretation seem appropriate to you or am I missing something?
>

I hope you are missing something :) But please elaborate so we can see.


>
> Thanks,
>
> - Pete
>
>
>
> On Tue, Feb 21, 2012 at 9:39 AM, Juan Sequeda <juanfederico@gmail.com>wrote:
>
>> Peter
>>
>> You may want to take a look at this:
>> http://www.ncbi.nlm.nih.gov/pubmed/21388572
>>
>> The implementation of the OBO to OWL mapping work is part of official
>> Gene Ontology project.
>>
>> Juan Sequeda
>> +1-575-SEQ-UEDA
>> www.juansequeda.com
>>
>>
>>
>> On Mon, Feb 20, 2012 at 7:46 PM, Peter DeVries <pete.devries@gmail.com>wrote:
>>
>>> How do OBO type ontologies work in the Linked Open Data cloud.
>>>
>>> One that I recently loaded has a large number of blank nodes.
>>>
>>> It the idea that these will be mapped to LOD URI's?
>>>
>>> Thanks,
>>>
>>> - Pete
>>>
>>> --
>>>
>>> ------------------------------------------------------------------------------------
>>> Pete DeVries
>>> Department of Entomology
>>> University of Wisconsin - Madison
>>> 445 Russell Laboratories
>>> 1630 Linden Drive
>>> Madison, WI 53706
>>> Email: pdevries@wisc.edu
>>> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
>>> Bases
>>> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>>>
>>> --------------------------------------------------------------------------------------
>>>
>>
>>
>
>
> --
>
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries@wisc.edu
> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
> Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>
> --------------------------------------------------------------------------------------
>
Received on Wednesday, 22 February 2012 05:28:43 UTC

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